C. elegans gro-1 gene

ABSTRACT

The invention relates to the identification of gro-1 gene and to demonstrate that the gro-1 gene is involved in the control of a central physiological clock. Also disclosed are four other genes located within the same operon as the gro-1 gene.

RELATED APPLICATIONS

This application is a continuation-in-part of PCT/CA98/00803 filed Aug.20, 1998, now at the national phase, and claiming priority on Canadianpatent application serial number 2,210,251 filed Aug. 25, 1997, nowabandoned.

BACKGROUND OF THE INVENTION

(a) Field of the Invention

The invention relates to the identification of gro-1 gene and four othergenes located within the same operon and to show that the gro-1 gene isinvolved in the control of a central physiological clock.

(b) Description of Prior Art

The gro-1 gene was originally defined by a spontaneous mutation isolatedfrom of a Caenorhabditis elegans strain that had recently beenestablished from a wild isolate (J. Hodgkin and T. Doniach, Genetics146: 149-164 (1997)). We have shown that the activity of the gro-1 genecontrols how fast the worms live and how soon they die. The time takento progress through embryonic and post-embryonic development, as well asthe life span of gro-1 mutants is increased (Lakowski and Hekimi,Science 272:1010-1013, (1996)). Furthermore, these defects arematernally rescuable: when homozygous mutants (gro-1/gro-1) derive froma heterozygous mother (gro-1/+), these animals appear to bephenotypically wild-type. The defects are seen only when homozygousmutants derive from a homozygous mother (Lakowski and Hekimi, Science272:1010-1013, (1996)). In general, the Properties of the gro-1 gene aresimilar to those of three other genes, clk-1, clk-2 and clk-3 (Wong etal., Genetics 139: 1247-1259 (1995); Hekimi et al., Genetics, 141:1351-1367 (1995); Lakowski and Hekimi, Science 272:1010-1013, (1996)),and this combination of phenotypes has been called the Clk (“clock”)phenotype. All four of these genes interact to determine developmentalrate and longevity in the nematode. Detailed examination of the clk-1mutant phenotype has led to the suggestion that there exists a centralphysiological clock which coordinates all or many aspects of cellularphysiology, from cell division and growth to aging. All four genes havea similar phenotype and thus appear to impinge on this physiologicalclock.

It would be highly desirable to be provided with the molecular identityof the gro-1 gene.

SUMMARY OF THE INVENTION

One aim of the present invention is to provide the molecular identity ofthe gro-1 gene and four other genes located within the same operon.

In accordance with the present invention there is provided a gro-1 genewhich has a function at the level of cellular physiology involved indevelopmental rate and longevity, wherein gro-1 is located within anoperon and gro-1 mutants have a longer life and a altered cellularmetabolism relative to the wild-type.

In accordance with a preferred embodiment, the gro-1 gene of the presentinvention codes for a GRO-1 protein having the amino acid sequence setforth in FIGS. 3A-3B (SEQ ID. NO:2).

The gro-1 gene is located within an operon which has the nucleotidesequence set forth in SEQ ID NO:1 and which also codes for four othergenes, referred as gop-1, gop-2, gop-3 and hap-1 genes.

In accordance with a preferred embodiment, the gop-1 gene of the presentinvention codes for a GOP-1 protein having the amino acid sequence setforth in FIGS. 13A-13C (SEQ ID. NO:4).

In accordance with a preferred embodiment, the gop-2 gene of the presentinvention codes for a GOP-2 protein having the amino acid sequence setforth in FIG. 14 (SEQ ID. NO:5).

In accordance with a preferred embodiment, the gop-3 gene of the presentinvention codes for a GOP-3 protein having the amino acid sequence setforth in FIGS. 15A-15B (SEQ ID. NO:6).

In accordance with a preferred embodiment, the hap-1 gene of the presentinvention codes for a HAP-1 protein having the amino acid sequence setforth in FIG. 16 (SEQ ID. NO:7).

In accordance with a preferred embodiment of the present invention, thegro-1 gene is of human origin and has the nucleotide sequence set forthin FIG. 8 (SEQ ID. NO:3).

In accordance with a preferred embodiment of the present invention,there is provided a mutant GRO-1 protein which has the amino acidsequence set forth in FIG. 3C.

In accordance with the present invention there is also provided a GRO-1protein which has a function at the level of cellular physiologyinvolved in developmental rate and longevity, wherein said GRO-1 proteinis encoded by the gro-1 gene identified above.

In accordance with a preferred embodiment of the present invention,there is provided a GRO-1 protein which has the amino acid sequence setforth in FIGS. 3A-3B (SEQ ID. NO:2).

In accordance with a preferred embodiment of the present invention,there is provided a GOP-1 protein which has the amino acid sequence setforth in FIGS. 13A-13C (SEQ ID. NO:4).

In accordance with a preferred embodiment of the present invention,there is provided a GOP-2 protein which has the amino acid sequence setforth in FIG. 14 (SEQ ID. NO:5).

In accordance with a preferred embodiment of the present invention,there is provided a GOP-3 protein which has the amino acid sequence setforth in FIGS. 15A-15B (SEQ ID. NO:6).

In accordance with a preferred embodiment of the present invention,there is provided a HAP-1 protein which has the amino acid sequence setforth in FIG. 16 (SEQ ID. NO:7).

In accordance with the present invention there is also provided a methodfor the diagnosis and/or prognosis of cancer in a patient, whichcomprises the steps of: a) obtaining a tissue sample from said patient;b) analyzing DNA of the obtained tissue sample of step a) to determineif the human gro-1 gene is altered, wherein alteration of the humangro-1 gene is indicative of cancer.

In accordance with the present invention there is also provided a mousemodel of aging and cancer, which comprises a gene knock-out of murinegene homologous to gro-1.

In accordance with the present invention there is provided the use ofcompounds interfering with enzymatic activity of GRO-1, GOP-1, GOP-2,GOP-3 or HAP-1 for enhancing longevity of a host.

In accordance with the present invention there is provided the use ofcompounds interfering with enzymatic activity of GRO-1, GOP-1, GOP-2,GOP-3 or HAP-1 for inhibiting tumorous growth.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A illustrates the genetic mapping of gro-1;

FIG. 1B illustrates the physical map of the gro-1 region;

FIG. 2A illustrates cosmid clones able to rescue the gro-1 (e2400)mutant phenotype;

FIG. 2B illustrates the genes predicted by Genefinder, the relevantrestriction sites and the fragments used to subclone the region;

FIGS. 3A-3C illustrate the genomic sequence and translation of the C.elegans gro-1 gene (SEQ. ID. NO:2);

FIG. 3D illustrates the predicted mutant protein;

FIG. 4A illustrates the five genes of the gro-1 operon (SEQ. ID. NO:1);

FIG. 4B illustrates the transplicing pattern of the five genes of thegro-1 operon;

FIG. 5A-5B illustrate the alignment of gro-1 with the publishedsequences of the E. coli (P16384) and yeast (P07884) enzymes;

FIG. 6 illustrates the biosynthetic step catalyzed by DMAPP transferase(MiaAp in E. coli, Mod5p in S. cerevisiae, and GRO-1 in C. elegans);

FIG. 7 illustrates the alignment of the predicted HAP-1 amino acidsequence with homologues from other species;

FIG. 8 illustrates the full mRNA sequence of human homologue of gro-1referred to as hgro-1 (SEQ. ID. NO:3);

FIG. 9A-9B illustrate a comparison of the conceptual amino acidsequences for GRO-1 and hgro-1p;

FIG. 10 illustrates a conceptual translation of a partial sequence ofthe Drosophila homologue of gro-1 (AA816785);

FIG. 11A-11B illustrate the structure of pMQ8;

FIG. 12 illustrates construction of pMQ18;

FIGS. 13A-13E illustrate the genomic sequence and translation of thegop-1 gene (SEQ. ID. NO:4);

FIG. 14A-14B illustrate the genomic sequence and translation of thegop-2 gene (SEQ. ID. NO:5);

FIGS. 15A-15D illustrate the genomic sequence and translation of thegop-3 gene (SEQ. ID. NO:6); and

FIG. 16A-16B illustrate the genomic sequence and translation of thehap-1 gene (SEQ. ID. NO:7).

DETAILED DESCRIPTION OF THE INVENTION

The gro-1 Phenotype

In addition to the previously documented phenotypes, we recently foundthat gro-1 mutants were temperature-sensitive for fertility. At 25° C.the progeny of these mutants is reduced so much that a viable straincannot be propagated. In contrast, gro-1 strains can easily bepropagated at 15 and 20° C.

We also discovered that the gro-1 (e2400) mutation increases theincidence of spontaneous mutations. As gro-1 (e2400) was originallyidentified in a non-standard background (Hodgkin and Doniach, Genetics146: 149-164 (1997)), we first backcrossed the mutations 8 times againstN2, the standard wild type strain. We then undertook to examine thegro-1 strain and N2 for the occurrence of spontaneous mutants whichcould be identified visually. We focused on the two class of mutantswhich are detected the most easily by simple visual inspection,uncoordinated mutants (Unc) and dumpy mutants (Dpy). We examined 8200wild type worms and found no spontaneous visible mutant. By contrast, wefound 6 spontaneous mutants among 12500 gro-1 mutants examined. Allmutants produced entirely mutant progeny indicating that they werehomozygous.

Sequences of All Primers Used Name Orientation Sequence (5′-3′) SEQ IDNO: SHP91 forward CGAACACTTTATATTTCTCG SEQ. ID. NO:8 SHP92 reverseGATAGTTCCCTTCGTTCGGG SEQ. ID. NO:9 SHP93 forward TTTCTGGATTTTAACCTTCCSEQ. ID. NO:10 SHP94 forward TTTCCGAGAAGTCACGTTGG SEQ. ID. NO:11 SHP95reverse TACAGGAATTTTTGAACGGG SEQ. ID. NO:12 SHP96 forwardCTTCAGATGACGTGGATTCC SEQ. ID. NO:13 SHP97 forward GGAATCCGAAAAAGTGAACTSEQ. ID. NO:14 SHP99 forward AAGAGATACACTCAATGGGG SEQ. ID. NO:15 SHP99reverse ATCGATACCACCGTCTCTGG SEQ. ID. NO:16 SHP109 reverseTTGAATCTACACTAATCACC SEQ. ID. NO:17 SHP100 reverse CCAATTATCTTTTCCAGTCASEQ. ID. NO:18 SHP110 forward ACATTATAAAGTTACTGTCC SEQ. ID. NO:19 SHP118forward TTTTAGTTAAAGCATTGACC SEQ. ID. NO:20 SHP119 reverseACATCTTTATCCATTTCTCC SEQ. ID. NO:21 SHP120 forward TGCAAAGGCTCTGGAACTCCSEQ. ID. NO:22 SHP129 reverse AAAAACCACTTGATATAAGG SEQ. ID. NO:23 SHP130reverse CATCCAAAAGCAGTATCACC SEQ. ID. NO:24 SHP134 forwardTTAATTGGATGCAAGCACCCC SEQ. ID. NO:25 SHP135 reverse ATTACTATACGAACATTTCCSEQ. ID. NO:26 SHP138 forward TTGTAAAGGCGTTAGTTTGG SEQ. ID. NO:27 SHP139forward CAGGAGTATTTGGTGATGCG SEQ. ID. NO:28 SHP140 forwardCGACGGGGAGAAGGTGACGG SEQ. ID. NO:29 SHP141 reverse AAAACTTCTACCAACAATGGSEQ. ID. NO:30 SHP142 reverse CGTAATCTCTCTCGATTAGC SEQ. ID. NO:31 SHP143reverse CCGTGGGATGGCTACTTGCC SEQ. ID. NO:32 SHP144 reverseTGGATTTGTGGCACGAGCGG SEQ. ID. NO:33 SHP145 reverse TTGATTGCCTCTCCTCGTCCSEQ. ID. NO:34 SHP146 reverse ATCAACATCTGATTGATTCC SEQ. ID. NO:35 SHP151forward CAGCGAGCGCATGCAACTATATATTGA SEQ. ID. NO:36 GCAGG SHP159 forwardAATAAATATTTAAATATTCAGATATACC SEQ. ID. NO:37 CTGAACTCTACAG SHP160 reverseAAACTGTAGAGTTCAGGGTATATCTGA SEQ. ID. NO:38 ATATTTAAATATTTATTC SHP161forward GTACGTGGAGCTCTGCAACTATATATT SEQ. ID. NO:39 GAGCAGG SHP162reverse ATGACACTGCAGGATAGTTCCCTTCGT SEQ. ID. NO:40 TCGGG SHP163 forwardGTGTTGCATCAGTTCATTCC SEQ. ID. NO:41 SHP164 forward GCTGTGCTAGAAGTCAGAGGSEQ. ID. NO:42 SHP165 reverse GTTCTCCTTGGAATTCATCC SEQ. ID. NO:43 SHP170reverse AGTATATCTAGATGTGCGAGTCTCTGC SEQ. ID. NO:44 CAATT SHP171 reverseAGTAATTGTACATTTAGTGG SEQ. ID. NO:45 SHP172 forward ATTAACCTTACTTACTTACCSEQ. ID. NO:46 SHP173 forward CTAAACTAAGTAATATAACC SEQ. ID. NO:47 SHP174reverse GTTGATTCTTTGAGCACTGG SEQ. ID. NO:48 SHP175 forwardAATTCGACCAATTACATTGG SEQ. ID. NO:49 SHP176 reverse AACATAGTTGTTGAGGAAGGSEQ. ID. NO:50 SHP177 forward AATTAATGGAGATTCTACGG SEQ. ID. NO:51 SHP178forward TCAGCATCTAGAAATGCAGG SEQ. ID. NO:52 SHP179 reverseCGAATGTCAACATTCACTGG SEQ. ID. NO:53 SHP180 forward CTTAACCTGATGTGTACTCGSEQ. ID. NO:54 SHP181 forward ATGAAGCTTTAGAGGATGCC SEQ. ID. NO:55 SHP182forward CGACGAATTTCTGGAGTCGG SEQ. ID. NO:56 SHP183 reverseACTGCATTATCCATTAATCC SEQ. ID. NO:57 SHP184 reverse CACCCAAATAACATCTATCCSEQ. ID. NO:68 SHP185 forward TTTAACCTCATCTTCGCTGG SEQ. ID. NO:59 SHP190forward ATGTTGCGCAAGCTTGGTTC SEQ. ID. NO:60 SL1 forwardTTTAATTACCCAAGTTTGAG SEQ. ID. NO:61 SL2 forward TTTTAACCCAGTTACTCAAGSEQ. ID. NO:62Positional Cloning of gro-1

gro-1 lies on linkage group III, very close to the gene clk-1 Togenetically order gro-1 with respect to clk-1 on the genetic map, 54recombinants in the dpy-17 to lon-1 interval were selected from amongthe self progeny of a strain which was unc-79(e1030)++clk-1(e2519)lon-1(e678)+/+dpy-17(e164) gro-1(e2400)+sma-4(e729). Three of theseshowed neither the Gro-1 nor the Clk-1 phenotypes, but carried unc-79and sma-4, indicating that these recombination events had occurredbetween gro-1 and clk-1. From the disposition of the markers, thisshowed that the gene order was dpy-17 gro-1 clk-1 lon-1, and thefrequency of events indicated that the gro-1 to clk-1 distance was 0.03map units. In this region of the genome, this corresponds to a physicalmap distance of ˜20 kb.

Several cosmids containing wild-type DNA spanning this region of thegenome were tested by microinjection into gro-1 mutants for theirability to complement the gro-1(e2400) mutation (FIG. 1). gro-1 wasmapped between dpy-17 and lon-1 on the third chromosome, 0.03 m.u. tothe left of clk-1 (FIG. 1A).

Based on the above genetic mapping, gro-1 was estimated to beapproximately 20 kb to the left of clk-1. Eight cosmids (represented bymedium bold lines) were selected as candidates for transformation rescue(FIG. 1B). Those which were capable of rescuing the gro-1(e2400) mutantphenotype are represented as heavy bold lines (FIG. 1B).

Of these, only B0498, C34E10 and ZC395 were able to rescue the mutantphenotype. Transgenic animals were fully rescued for developmentalspeed. In addition, the transgenic DNA was able to recapitulate thematernal rescue seen with the wild-type gene, that is, mutants notcarrying the transgenic DNA but derived from transgenic mothers displaya wild type phenotype. The 7 kb region common to the three rescuingcosmids had been completely sequenced, and this sequence was publiclyavailable.

We generated subclones of ZC395 and assayed them for rescue (FIG. 2).The common 6.5 kb region is blown up in part B. B0498 has not beensequenced and therefore its ends can not be positioned and are thereforerepresented by arrows.

One subclone pMQ2, spanned 3.9 kb and was also able to completely rescuethe growth rate defect and recapitulate the maternal effect. Thesequences in pMQ2 potentially encodes two genes. However, a secondsubclone, pMQ3, which contained only the first of the potential genes(named ZC395.7 in FIG. 2A), was unable to rescue.

Furthermore, frameshifts which would disrupt each of the two genes'coding sequences were constructed in pMQ2 and tested for rescue.Disruption of the first gene (in pMQ4) did not eliminate rescuingability, but disruption of the second gene (in pMQ5) did. This indicatesthat the gro-1 rescuing activity is provided by the second predictedgene.

pMQ2 was generated by deleting a 29.9 kb SpeI fragment from ZC395,leaving the left-most 3.9 kb region containing the predicted genesZC395.7 and ZC395.6 (FIG. 2B). pMQ3 was created in the same fashion, bydeleting a 31.4 kb NdeI fragment from ZC395, leaving only ZC395.7intact. In pMQ4, a frameshift was induced in ZC395.7 by degrading the 4bp overhang of the ApaI site. A frameshift was also induced in pMQ5 byfilling in the 2 bp overhang of the NdeI site found in the second exonof ZC395.6. These frameshifts presumably abolish any function of ZC395.7and ZC395.6 respectively. The dotted lines represent the extent offrameshift that resulted from these alterations.

To establish the splicing pattern of this gene, cDNAs encompassing the5′ and 3′ halves of the gene were produced by reverse transcription-PCRand sequenced (FIG. 3).

This revealed that the gene is composed of 9 exons, spans ˜2 kb, andproduces an mRNA of 1.3 kb. To confirm that this is indeed the gro-1gene, genomic DNA was amplified by PCR from a strain containing thegro-1(e2400) mutation and the amplified product was sequenced. A lesionwas found in the 5th exon, where a 9 base-pair sequence has beenreplaced by a 2 base-pair insertion, leading to a frameshift (FIG. 3C).FIG. 3C illustrates those residues which differ from wild type are inbold.

The reading frame continues out-of-frame for another 33 residues beforeterminating.

FIGS. 3A-B illustrate the coding sequence in capital letters, while theintrons, and the untranslated and intergenic sequence are in lower caseletters. The protein sequence is shown underneath the coding sequence.Position 1 of the nucleotide sequence is the first base after the SL2trans-splice acceptor sequence. Position 1 of the protein sequence isthe initiator methionine. All PCR primers used for genomic and cDNAamplification are represented by arrows. For primers extendingdownstream (arrows pointing right) the primer sequence correspondsexactly to the nucleotides over which the arrow extends. But for primersextending upstream (arrows pointing left) the primer sequence isactually the complement of the sequence under the arrow. In both casesthe arrow head is at the 3′ end of the primer. The sequence of the twoprimers which flank gro-1 (SHP93 and SHP92) are not represented in thisfigure. Their sequences are: SHP93 TTTCTGGATTTTAACCTTCC (SEQ. ID. NO:10)and SHP92 GATAGTTCCCTTCGTTCGGG (SEQ. ID. NO:9). The wild type splicingpattern was determined by sequencing of the cDNA. Identification of thee2400 lesion was accomplished by sequencing the e2400 allele. The e2400lesion consists of a 9 bp deletion and a 2 bp insertion at position1196, resulting in a frameshift.

gro-1 is Part of a Complex Operon (FIGS. 3A-3B)

Amplification of the 5′ end of gro-1 from cDNA occurred only when thetrans-spliced leader SL2 was used as the 5′ primer, and not when SL1 wasused. SL2 is used for trans-splicing to the downstream gene when twogenes are organized into an operon (Spieth et al., Cell 73: 521-532(1993); Zorio et al., Nature 372: 270-272 (1994)). This indicates thatat least one gene upstream of gro-1 is co-transcribed with gro-1 from acommon promoter. We found that sequences from the 5′ end of the threenext predicted genes upstream of gro-1 (ZC395.7, C34E10.1, and C34E10.2)all could only be amplified with SL2. Sequences from the fourthpredicted upstream gene (C34E10.3), however, could be amplified withneither spliced leader, suggesting that it is not trans-spliced. Thedistance between genes in operons appear to have an upper limit (Spiethet al., Cell 73: 521-532 (1993); Zorio et al., Nature 372: 270-272(1994)), and no gene is predicted to be close enough upstream ofC34E10.3 or downstream of gro-1 to be co-transcribed with these genes.Our findings suggest therefore that gro-1 is the last gene in an operonof five co-transcribed genes (FIG. 4).

Nested PCR was used to amplify the 5′ end of each gene. SL1 or SL2specific primers were used in conjunction with a pair of gene-specificprimers. cDNA generated by RT-PCR using mixed stage N2 RNA was used astemplate in the nested PCR. FIG. 4A illustrates a schematic of the gro-1operon showing the coding sequences of each gene and the primers(represented by flags) used to establish the trans-splicing patterns.

FIG. 4B illustrates the products of the PCR with SL1 and SL2 specificprimers for each of the five genes. The sequences of the primers usedare as follows: SL1: TTTAATTACCCAAGTTTGAG, (SEQ. ID. NO:61) SL2:TTTTAACCCAGTTACTCAAG, (SEQ. ID. NO:62) SHP141: AAAACTTCTACCAACAATGG,(SEQ. ID. NO:30) SHP142: CGTAATCTCTCTCGATTAGC, (SEQ. ID. NO:31) SHP143:CCGTGGGATGGCTACTTGCC, (SEQ. ID. NO :32) SHP144: TGGATTTGTGGCACGAGCGG,(SEQ. ID. NO:33) SHP145: TTGATTGCCTCTCCTCGTCC, (SEQ. ID. NO:34) SHP146:ATCAACATCTGATTGATTCC, (SEQ. ID. NO:35) SHP130: CATCCAAAAGCAGTATCACC,(SEQ. ID. NO:24) SHP119: ACATCTTTATCCATTTCTCC, (SEQ. ID. NO:21) SHP95:TACAGGAATTTTTGAACGGG, (SEQ. ID. NO:12) SHP99: ATCGATACCACCGTCTCTGG.(SEQ. ID. NO:16)

The gene immediately upstream of gro-1, has homology to the yeast geneHAM1, and we have renamed the gene hap-1. We have established itssplicing pattern by reverse transcription PCR and sequencing. Thisrevealed that hap-1 is composed of 5 exons and produces an mRNA of 0.9kb. We also found that sequences which were predicted to belong toZC395.7 (now hap-1) are in fact spliced to the exons of C34E10.1. Thisis consistent with our finding that hap-1 is SL2 spliced as it puts theend of the C34E10.1 very close to the start of hap-1 (FIG. 4).

The gro-1 Gene Product

Conceptual translation of the gro-1 transcript indicated that it encodesa protein of 430 amino acids highly similar to a strongly conservedcellular enzyme: dimethylallyldiphosphate:tRNA dimethylallyltransferase(DMAPP transferase). FIG. 5 shows an alignment of gro-1 with thepublished sequences of the E. coli (P16384) and yeast (P07884) enzymes.Residues where the biochemical character of the amino acids is conservedare shown in bold. Identical amino acids are indicated further with adot. The ATP/GTP binding site and the C2H2 zinc finger site arepredicted and not experimental. The point at which the gro-1 (e2400)mutation alters the reading frame of the sequence is shown. The twoalternative initiatior methionines in the yeast sequence, and theputative corresponding methionines in the worm sequence, are underlined.

Database searches also identified a homologous human expressed sequencetag (Genbank ID: Z40724). The human clone has been used to derive asequence tagged site (STS). This means that the genetic and physicalposition of the human gro-1 homologue is known. It maps to chromosome 1,122.8 cR from the top of Chr 1 linkage group and between the markersD1S255 and D1S2861. This information was found in the UniGene databaseor the National Center for Biotechnology Information (NCBI). We havesequenced Z40724 by classical methods but found that Z40724 is not afull length cDNA clone as it does not contain an initiator methioninenor the poly A tail. We used the sequence of Z40724 to identify furtherclones by database searches. We found one clone (Genbank ID: AA332152)which extended the sequence 5′ by 28 nucleotides, as well as one clone(Genebank ID: AA121465) which extended the sequence substantially in the3′ direction but didn't include the poly A tail. We then used AA121465to identify an additional clone (AA847885) extending the sequence to thepoly A tail. FIG. 8 shows the full sequence with the putative initiatorATG shown in bold and the sequence of Z60724 is shown underlined. Acomparison of the conceptual amino acid sequences for GRO-1 and hgro-1pis shown in FIG. 9. Amino acid identities are indicated by a dot. Bothsequences contain a region with a zinc finger motif which is shownunderlined.

An additional metazoan homologue is represented by Drosophila EST:Genbank accession: AA816785. In E. coli and other bacteria, the geneencoding DMAPP transferase is called miaA (a.k.a trpx) and is calledmod5 in yeast. DMAPP transferase catalyzes the modification of adenosine37 of tRNAs whose anticodon begins with U (FIG. 6).

In these organisms the enzyme has been shown to usedimethylallyldiphosphate as a donor to generate dimethylallyl-adenosine(dma⁶A37), one base 3′ to the anticodon (for review and biochemicalcharacterization of the bacterial enzyme see Persson et al., Biochimie76: 1152-1160 (1994); Leung et al., J Biol Chem 272: 13073-13083 (1997);Moore and Poulter, Biochemistry 36:604-614 (1997)). In earlierliterature this modification is often referred to as isopentenyladenosine (i⁶A37).

The high degree of conservation of the protein sequence between GRO-1and DMAPP in S. cerevisiae and E. coli suggest that GRO-1 possesses thesame enzymatic activity as the previously characterized genes. Thesequence contains a number of conserved structural motifs (FIG. 5),including a region with an ATP/GTP binding motif which is generallyreferred to as the ‘A’ consensus sequence (Walker et al., EMBO J 1:945-951 (1982)) or the ‘P-loop’ (Saraste et al., Trends Biochem Sci 15:430-434 (1990)).

In addition, at the C-terminal end of the GRO-1 sequence, there is aC2H2 zinc finger motif as defined by the PROSITE database. This type ofDNA-binding motif is believed to bind nucleic acids (Klug and Rhodes,Trends Biochem Sci 12: 464-469 (1987)). Although there appears to besome conservation between the worm and yeast sequences in the C-terminusend of the protein (FIG. 5), including in the region encompassing thezinc finger in GRO-1, the zinc finger motif per se is not conserved inyeast but is present in humans (FIG. 9).

In yeast DMAPP transferase is the product of the MOD5 gene, and existsin two forms: one form which is targeted principally to themitochondria, and one form which is found in the cytoplasm and nucleus.These two forms differ only by a short N-terminal sequence whosepresence or absence is determined by differential translation initiationat two “in frame” ATG codons. (Gillman et al., Mol & Cell Biol 11:2382-90 (1991)). The gro-1 open reading frame also contains two ATGcodons at comparable positions, with the coding sequence between the twocodons constituting a plausible mitochondrial sorting signal (FIGS. 3and 5). It is likely therefore that DMAPP transferase in worms alsoexists in two forms, mitochondrial and cytoplasmic.

It should be noted, however, that the sequence of hgro-1 shows only onein-frame methionine before the conserved ATP/GTP binding site (FIG. 9).As we cannot be assured to have determined the sequence of the fulllength transcript, it is possible that further 5′ sequence might revealan additional methionine. Alternatively, in humans, the mechanism bywhich the enzyme is targeted to several compartments might not involveddifferential translation initiation. In this context, it should be notedthat the sorting signals which can be predicted from the sequence ofhgro-1p are predicted to be highly ambiguous by the prediction programPSORT II. Furthermore, a conceptual translation of the Drosophilasequence (AA816785) predicts only one initiator methionine before theATP/GTP binding site as well as several in-frame stop codons upstream ofthis start (FIG. 10), suggesting that no additional upstream ATG couldserve as translation initiation site. In the figure, stop codons areindicated by stop, methionines are indicated by Met, and the conservedATP/GTP binding site is underlined.

Expression Pattern of GRO-1

We have also constructed a reporter gene expressing a fusion proteincontaining the entire GRO-1 amino acid sequence fused at the C-terminalend to green fluorescent protein (GFP). The promotor of the reportergene is the sequence upstream of gop-1 (FIGS. 13A-13C), the first genein the operon (see FIG. 4). The promotor sequence is 306 bp longstarting 32 nucleotides upstream of the gop-1 ATG. It is fused at theexact level upstream of gro-1 where trans-splicing to SL2 normalyoccurs.

The genes gop-2 (FIG. 14) and gop-3 (FIGS. 15A-15B) are also located inthe operon (see FIG. 4), the second and third genes in the operon.

We first construct the clone pMQ8 in which gro-1 is directly under thepromoter for the whole operon using the hybrid primers SHP160 (SEQ. ID.NO:38) and SHP159 (SEQ. ID. NO:37) and the flanking primers SHP161 (SEQ.ID. NO:39) and SHP162 (SEQ. ID. NO:40) in sequential reactions eachfollowed by purification of the products and finally cloning into pUC18(FIG. 11).

Primers SHP151 (SEQ. ID. NO:36) and SHP170 (SEQ. ID. NO:44) where thenused to amplify part of the insert in pMQ8 and clone in pPD95.77 (giftfrom Dr Andrew Fire) which was designed to allow a protein of interestto be transcriptionally fused to Green Fluorescent Protein (GFP) (FIG.12).

The reporter construct fully rescues the phenotype of a gro-1 (e2400)mutant upon injection and extrachromosomal array formation, indicatingthat the fusion to the GFP moiety does not significantly inhibit thefunction of GRO-1. Fluorescent microscopy indicated that gro-1 isexpressed in most or all somatic cells. Furthermore, the GRO-1::GFPfusion protein is localized in the mitochondria, in the cytoplasm aswell as in the nucleus.

The hap-1 Gene Product (FIG. 16)

hap-1 is homologous to the yeast gene HAM1 as well as to sequences inmany organisms including bacteria and mammals (FIG. 7).

The origin of the worm and yeast sequence is as described above andbelow. The human sequence was inferred from a cDNA sequence assembledfrom expressed sequence tags (ESTs); the accession numbers of thesequences used were: AA024489, AA024794, AA025334, AA026396, AA026452,AA026502, AA026503, AA026611, AA026723, AA035035, AA035523, AA047591,AA047599, AA056452, AA115232, AA115352, AA129022, AA129023, AA159841,AA160353, AA204926, AA226949, AA227197 and D20115. The E. coli sequenceis a predicted gene (accession 1723866).

Mutations in HAM1 increase the sensitivity of yeast to the mutageniccompound 6-N-hydroxylaminopurine (HAP), but do not increase spontaneousmutation frequency (Nostov et al., Yeast 12:17-29 (1996)). HAP is ananalog of adenine and in vitro experiments suggest that the mechanism ofHAP mutagenesis is its conversion to a deoxynucleoside triphosphatewhich is incorporated ambiguously for dATP and dGTP during DNAreplication (Abdul-Masih and Bessman, J Biol Chem 261 (5): 2020-2026(1986)). The role of the Ham1p gene product in increasing sensitivity toHAP remains unclear.

Explaining the Pleiotropy of miaA and gro-1

Mutations in miaA, the bacterial homologue of gro-1, show multiplephenotypes and affect cellular growth in complex ways. For example, inSalmonella typhimurium, such mutations result in 1) a decreased efficacyof suppression by some suppressor tRNA, 2) a slowing of ribosomaltranslation, 3) slow growth under various nutritional conditions, 4)altered regulation of several amino acid biosynthetic operons, 5)sensitivity to chemical oxidants and 6) temperature sensitivity foraerobic growth (Ericson and Björk, J. Bacteriol. 166: 1013-1021 (1986);Blum, J. Bacteriol. 170: 5125-5133 (1988)). Thus, MiaAp appears to beimportant in the regulation of multiple parallel processes of cellularphysiology. Although we have not yet explored the cellular physiology ofgro-1 mutants along the lines which have been pursued in bacteria, theapparently central role of miaA is consistent with our findings thatgro-1, and the other genes with a Clk phenotype, regulate many disparatephysiological and metabolic processes in C. elegans (Wong et al.,Genetics 139: 1247-1259 (1995); Lakowski and Hekimi, Science 272:1010-1013 (1996); Ewbank et al., Science 275: 980-983 (1997)).

In addition to the various phenotypes discussed above, miaA mutationsincrease the frequency of spontaneous mutations (Connolly and Winkler, JBacteriol 173(5):1711-21 (1991); Connolly and Winkler, J Bacteriol 171:3233-46 (1989)). As described in the previous section we havepreliminary evidence that gro-1 (e2400) also increases the frequency ofspontaneous mutations in worms.

How can the alteration in the function of MDAPP transferase result in somany distinct phenotypes? Bacterial geneticists working with miaA havegenerally suggested that this enzyme and the tRNA modification itcatalyzes have a regulatory function which is mediated throughattenuation (e.g. Ericson and Björk, J. Bacteriol. 166: 1013-1021(1986)). Attenuation is a phenomenon by which the transcription of agene is interrupted depending on the rate at which ribosomes cantranslate the nascent transcript. Ribosomal translation is slowed inmiaA mutants, and thus, through an effect on attenuation, could affectthe expression of many genes whose expression is regulated byattenuation.

gro-1 (e2400) also produces pleiotropic effects and, in addition,displays a maternal-effect, suggesting that it is involved in aregulatory process (Wong et al., Genetics 139: 1247-1259 (1995).However, attenuation involves the co-transcriptional translation ofnascent transcripts, which is not possible in eukaryotic cells weretranscription and translation are spatially separated by the nuclearmembrane. If the basis of the pleiotropy in miaA and gro-1 is the same,then a mechanism distinct from attenuation has to be involved. Below weargue that this mechanism could be the modification by DMAPP transferaseof adenine residues in DNA in addition to modification of tRNAs.

A Role for gro-1 in DNA Modification?

We observed that gro-1 can be rescued by a maternal effect, so thatadult worms homozygous for the mutation, but issued from mother carryingone wild type copy of the gene display a wild type phenotype, in spiteof the fact that such adults are up to 1000 fold larger than the eggproduced by their mother. It is unlikely that enough wild type productcan be deposited by the mother in the egg to rescue a adult which is1000 times larger. This observation suggests therefore that gro-1 caninduce an epigenetic state which is not altered by subsequent somaticgrowth. One of the best documented epigenetic mechanisms is imprintingin mammals (Lalande, Annu Rev Genet 30: 173-196 (1996)) which isbelieved to rely on the differential methylation of genes (Laird andJaenisch, Annu Rev Genet 30: 441-464; Klein and Costa, Mutat Res 386:103-105 (1997)). Modification of bases in DNA have also been linked toregulation of gene expression in the protozoan Trypanosoma brucei. Thepresence of beta-D-glucosyl-hydroxy-methyluracil in the long telomericrepeats of T. brucei correlates with the repression of surface antigengene expression (Goatiners-Ampt et al., Cell 75: 112-1136 (1993); vanLeeuwen et al., Nucleic Acids Res 24: 2476-2482 (1996)).

gro-1 and miaA increase the rate of spontaneous mutations, which isgenerally suggestive of a role in DNA metabolism, and can be related tothe observation that methylation is linked to spontaneous mutagenesis,genome instability, and cancer (Jones and Gonzalgo, Proc. Natl. Acad.Sci. USA, 94: 2103-2105 (1997)).

Does gro-1 have access to DNA? Studies with mod5, the yeast homologue ofgro-1, have shown that there are two forms of Mod5p, one is localized tothe nucleus as well as to the cytoplasm, and the other form is localizedto the mitochondria as well as the cytoplasm (Boguta et al., Mol. Cell.Biol. 14: 2298-2306 (1994)). The nuclear localization is striking asisopentenylation of nuclear-encoded tRNA is believed to occurexclusively in the cytoplasm (reviewed in Boguta et al., Mol. Cell.Biol. 14: 2298-2306 (1994)). Furthermore, studies of a gene maf1 haveshown that when mod5 is mislocalized to the nucleus, the efficiency ofcertain suppressor tRNA is decreased, an effect known to be linked tothe absence of the tRNA modification (Murawski et al., Acta Biochim.Pol. 41: 441-448 (1994)). Finally, as described in the previous section,gro-1 contains a zinc finger, a nuclei acid binding motif. The zincfinger could bind tRNAs, but as it is in the C-terminal domain of gro-1and human hgro-1 that has no equivalent in miaA, it is clearly notnecessary for the basic enzymatic function. We speculate that it mightbe necessary to increase the specificity of DNA binding in the largemetazoan genome. It should also be noticed that the second form of Mod5pwhich is localized to mitochondria also has the opportunity to bind andpossibly modify DNA as it has access to the mitochondrial genome. Seethe previous section entitled “A role for gro-1 in a central mechanismof physiological coordination” for an alternative possibility as to thefunction of GRO-1 in the nucleus.

miaA and gro-1 are Found in Complex Operons

We have found that gro-1 is part of a complex operon of five genes (FIG.4). It is believed that genes are regulated coordinately by singlepromoters when they participate in a common function (Spieth et al.,Cell 73: 521-532 (1993)). In some cases, this is well documented. Forexample, the proteins LIN-15A and LIN-15B which are both required forvulva formation in C. elegans, are unrelated products from two genestranscribed in a common operon (Huang et al., Mol Biol Cell 5(4):395-411 (1994)). One of the genes in the gro-1 promoter is hap-1, whoseyeast homologue has been shown to be involved in the control ofmutagenesis (Nostov et al., Yeast 12: 17-29 (1996)). Under thehypothesis that gro-1 modifies DNA, it suggest an involvement of hap-1in this or similar processes. The presence in the same operon alsosuggest that all five genes might collaborate in a common function. Thephenotype of gro-1 suggests that this function is regulatory. In thiscontext, it should be noted that miaA also is part of a particularlycomplex operon (Tsui and Winkler, Biochimie 76: 1168-1177 (1994)),although, except for miaA/gro-1, there are no other homologous genes inthe two operons.

A Role for gro-1 in a Central Mechanism of Physiological Coordination

We have speculated that the genes with a Clk phenotype might participatein a central mechanism of physiological coordination, probably includingthe regulation of energy metabolism. clk-1 encodes a mitochondrialprotein (unpublished observations), and its homologue in yeast has alsobeen shown to be mitochondrial (Jonassen, T (1998) Journal of BiologicalChemistry 273:3351-3357). The yeast clk-1 homologue is involved in theregulation of the biosynthesis of ubiquinone (Marbois, B. N. and Clarke,C. F. (1996) Journal of Biological Chemistry 271:2995-3004). Ubiquinone,also called coenzyme Q, is central to the production of ATP inmitochondria. In worms, however, we have found that clk-1 is notstrictly required for respiration. How might gro-1 fit into thispicture?

One link is that dimethylallyldiphosphate is known to be the precursorof the lipid side-chain of ubiquinone. In bacteria, ubiquinone is themajor lipid made from DMAPP. In eukaryotes cholesterol and itsderivatives are also made from DMAPP. Interestingly, C. elegans requirescholesterol in the growth medium for optimal growth. This link, however,remains tenuous, in particular in the absence of an understanding of thebiochemical function of CLK-1.

In several bacteria, the adenosine modification carried out by DMAPPtransferase is only the first step in a series of further modificationof this base (Persson et al., Biochimie 76: 1152-1160 (1994)). Theseadditional modifications have been proposed to play the role of a sensorfor the metabolic state of the cell (Buck and Ames, Cell 36: 523-531(1984); Persson and Björk, J. Bacteriol. 175: 7776-7785 (1993)). Forexample, one of the subsequent steps, the synthesis of2-methylthio-cis-ribozeatin is carried out by a hydroxylase encoded bythe gene miaE. When the cells lack miaE they become incapable of usingintermediates of the citric acid cycle such as fumarate and malate asthe sole carbon source.

Another link to energy metabolism springs from the recent biochemicalobservations of Winkler and co-workers using purified DMAPP transferase(E. coli MiaAp) (Leung et al., J Biol Chem 272: 13073-13083 (1997)).These investigators observed that the enzyme in competitively inhibitedby phosphate nucleotides such as ATP or GTP. Furthermore, using theirestimation of K_(m) of the enzyme and its concentration in the cell,they calculate that the level of inhibition of the enzyme in vivo, wouldexactly allow the enzyme to modify all tRNAs but any further inhibitionwould leave unmodified tRNAs. This suggests that the exact level ofmodification of tRNA (or of DNA) could be exquisitely sensitive to thelevel of phosphate nucleotides. Superficially, this is consistent withthe phenotypic observations. The state of mutant cells which lack DMAPPtransferase entirely would be equivalent of cells where very high levelsof ATP would completely inhibit the enzyme. Such cells might thereforeturn down the ATP generating processes in response to the signalprovided by undermodified tRNAs (or DNA).

More generally, GRO-1 could act in the crosstalk between nuclear andmitochondrial genomes. The nuclear and mitochondrial genomes bothcontribute gene products to the mitochondrion energy-producing machineryand these physically separate genomes must therefore exchangeinformation somehow to coordinate their contributions (reviewed inPoyton, R. O. and McEwen J. E. (1996) Annu. Rev. Biochem. 65:563-607).Furthermore, the energy producing activity of the mitochondria isessential to the rest of the cell, and the needs of a particular cell ata particular time must be somehow convey to the organelle to regulateits activity. GRO-1 could participate in this coordination in thefollowing manner. GRO-1 is found in three compartments, the nucleus, thecytoplasm and the mitochondria (see above), and thus has the opportunityto regulate gene expression in more that one way. How could its actioncoordinate gene expression between compartment? GRO-1 could partitionbetween the mitochondria and the nucleus and its relative distributioncould be determined by the amount of RNA (or mtDNA) in the mitonchodria(Parikh, V. S. et al. (1987) Science 235:576-580). For example, if thecell is rich in mitochondria, much GRO-1 will be bound there which couldresult in a relative depletion of activity in the cytoplasm withregulatory consequences on the translation machinery. Binding of GRO-1in the nucleus could have similar consequences and provide informationabout nuclear gene expression to the translation machinery.

While the invention has been described in connection with specificembodiments thereof, it will be understood that it is capable of furthermodifications and this application is intended to cover any variations,uses, or adaptations of the invention following, in general, theprinciples of the invention and including such departures from thepresent disclosure as come within known or customary practice within theart to which the invention pertains and as may be applied to theessential features hereinbefore set forth, and as follows in the scopeof the appended claims.

1. A gro-1 gene which has a function at the level of cellular physiologyinvolved in developmental rate and longevity, wherein gro-1 mutationscause a longer life and an altered cellular metabolism relative to thewild-type, wherein gro-1 gene has the identifying characteristics ofnucleotide sequence set forth in SEQ ID NO:3.
 2. The gro-1 gene of claim1, which codes for a GRO-1 protein having the amino acid sequence setforth in FIGS. 9A-9B as deduced from SEQ ID NO:3.
 3. A gro-1co-expressed gene which comprises a gop-1 gene which codes for a GOP-1protein having the amino acid sequence set forth in FIGS. 13A-13C (SEQID. NO:4); wherein said gop-1 gene is located in the gro-1 operon andsaid gop-1 gene is transcriptionally co-expressed with gro-1 genepresent in said operon.
 4. A gro-1 co-expressed gene which comprises agop-2 gene which codes for a GOP-2 protein having the amino acidsequence set forth in FIGS. 14A-B (SEQ ID. NO:5); wherein said gop-2gene is located in the gro-1 operon and said gop-2 gene istranscriptionally co-expressed with gro-1 gene present in said operon.5. A gop-3 gene which codes for a GOP-3 protein having the amino acidsequence set forth in FIGS. 15A-15B (SEQ ID. NO:6); wherein said gop-3gene is located in the gro-1 operon and said gop-3 gene istranscriptionally co-expressed with gro-1 gene present in said operon.6. A hap-1 gene which codes for a HAP-1 protein having the amino acidsequence set forth in FIGS. 16A-B (SEQ ID. NO:7); wherein said hap-1gene is located in the gro-1 operon and said hap-1 gene istranscriptionally co-expressed with gro-1 gene present in said operon.7. A GRO-1 protein which has a function at the level of cellularphysiology involved in developmental rate and longevity, wherein saidGRO-1 protein is encoded by the gene of claims 1 and
 2. 8. A mutantGRO-1 protein which has the amino acid sequence set forth in FIG. 3D. 9.A GRO-1 protein which has the amino acid sequence set forth in FIGS.3A-3C (SEQ ID. NO:2).
 10. A GRO-1 co-expressed protein which comprises aGOP-1 protein encoded by the gene according to claim 3; wherein saidprotein which has the amino acid sequence set forth in FIGS. 13A-13C(SEQ ID. NO:4) and human homolog thereof.
 11. A GRO-1 co-expressedprotein which comprises a GOP-2 protein encoded by the gene according toclaim 4; wherein said protein which has the amino acid sequence setforth in FIG. 14 (SEQ ID. NO:5) and human homolog thereof.
 12. A GOP-3protein encoded by the gene according to claim 5; wherein said proteinwhich has the amino acid sequence set forth in FIGS. 15A-15B (SEQ ID.NO:6) and human homolog thereof.
 13. A HAP-1 protein encoded by the geneaccording to claim 6; wherein said protein which has the amino acidsequence set forth in FIG. 16 (SEQ ID. NO:7).
 14. A method for thediagnosis and/or prognosis of cancer in a patient, which comprises thesteps of: a) obtaining a tissue sample from said patient; b) analyzingDNA of the obtained tissue sample of step a) to determine if the humangro-1 gene is altered, wherein alteration of the human gro-1 gene isindicative of cancer.
 15. A mouse model of aging and cancer, whichcomprises a gene knock-out of murine gene homologous to gro-1 gene ofclaims 1 and
 2. 16. A method of regulating physiological processes oftissues, organs and/or whole organism of a host which comprises acompound interfering with enzymatic activity of GRO-1 of claim 7, 8 or9.
 17. A method of regulating physiological processes of tissues, organsand/or whole organism of a host which comprises a compound interferingwith enzymatic activity of GOP-1 of claim
 10. 18. A method of regulatingphysiological processes of tissues, organs and/or whole organism of ahost which comprises a compound interfering with enzymatic activity ofGOP-2 of claim
 11. 19. A method of regulating physiological processes oftissues, organs and/or whole organism of a host which comprises acompound interfering with enzymatic activity of GOP-3 of claim
 12. 20. Amethod of regulating physiological processes of tissues, organs and/orwhole organism of a host which comprises a compound interfering withenzymatic activity of HAP-1 of claim 13.